Mutants of MAW motifs of RecA protein homologs method of making them, and their uses

ABSTRACT

RecA protein mutants and RecA homolog protein mutants which contain one or more mutations in the MAW motif are presented. The mutants rely on replacement of wildtype amino acid residues in the MAW motif with specific replacement residues to alter the three-dimensional structure of the MAW motif and to change the protein&#39;s DNA-binding properties. Three classes of mutants are described: mutants which will reduce the protein&#39;s dependence on ATP to initiate DNA-binding; mutants which more tightly bind DNA; and combination mutants which possess both of these properties.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.60/094,071, filed Jul. 24, 1998.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

The U.S. Government has a paid-up license in this invention and theright in limited circumstances to require the patent owner to licenseothers on reasonable terms as provided for by the terms of Grant No. GM32355 awarded by NIH.

BACKGROUND OF THE INVENTION

(1) Field of the Invention

The invention concerns the invention and production of mutant RecAhomolog proteins by substituting amino acid residues at particularresidue positions along the MAW (Makes ATP Work) motif. The MAW motif isdefined as amino acid residues 40 to 65 in the Escherichia coli (E.coli) RecA protein (SEQ ID NO: 1) and the homologs of this structure inother proteins. These mutants are classified as Class V, VI, and VIImutants. Class V mutants of this form can be active independently ofATP, which is required to activate wildtype RecA. Class VI mutants ofthis form can exhibit tighter binding to DNA than wildtype RecA. ClassVII mutants exhibit combinations of Class V and VI mutant properties toprovide both ATP-independence and tighter DNA binding.

(2) Description of the Related Art

The RecA protein of E. coli is an important player in the in vivoprocesses of homologous recombination and recombinational DNA repair.Its functions in vivo depend upon several key activities identified invitro, including the binding of multiple DNA molecules and thehydrolysis of ATP. Such ligand interactions allow the detection ofcomplementary sequences between homologous DNA molecules, generating aHolliday-like structure after strands are exchanged. The RecA proteinalso promotes branch point migration to resolve this intermediatestructure.

Nature also highlights the significant role of the RecA protein by usingit as the regulator of the SOS response. (Friedberg, et al., in DNARepair and Mutagenesis, ASM Press, Washington, D.C. 1995, p. 407) Theexistence of damaged DNA signals the RecA protein to become activated.This switch promotes the autoproteolysis of the LexA repressor uponbinding to a RecA-DNA-ATP complex. Once the LexA repressor isinactivated, a number of protein products are produced, including theRecA protein. Many of these SOS proteins act at the site of DNA damageafter the RecA protein has initiated the repair process throughrecombinational DNA repair. Thus, the RecA protein is an importantgenomic sentinel for E. coli since it identifies problems and organizestheir correction—all of which ensures the integrity of an organism'sgenetic information.

One relatively unexplored region of the RecA protein is the recentlydefined MAW (Makes ATP Work) motif, located at residues 40-65. It hasbeen proposed that this is part of the conformational switch of the RecAprotein that signals the ADP- vs ATP-bound state. It is well establishedthat the RecA protein exhibits different conformations in response tocofactors. (Egelman & Stasiak, Micron 24:309 (1993)).

There are some known mutations of RecA and homologous proteins, withinthe MAW motif and elsewhere, which relate to either ATP interaction orDNA binding. S. Sommer, F. Boudsocq, R. Devoret, and A. Bailone,Specific RecA Amino Acid Changes Affect RecA-UmuD'C Interaction,Molecular Microbiology 28:281 (1998) discloses a mutation within the MAWmotif, substituting leucine for serine at position 44 (44SL) (Mutantsare herein denoted by the position number, the letter designation of theremoved residue, and the letter designation of the substituted residue;thus, “44SL” denotes a serine to leucine switch at position 44). Thismutation was isolated randomly through a genetic screen. The in vivophenotype shows that the mutant behaves like wildtype RecA proteinexcept when it interacts with E. coli protein UmuD'C. Biochemicalinformation regarding the characteristics of 44SL is not available.

P. Howard-Flanders and L. Theriot, Mutants of Escherichia coli K-12Defective in DNA Repair and in Genetic Recombination, Genetics 53:1137(1966) discloses a substitution of leucine to phenylalanine at position51(51 LF) within the MAW motif in RecA 13. This mutation was shown to beinactive in vivo. Further, S. D. Lauder and S. C. Kowalczykowski,Negative Co-dominant Inhibition of RecA Protein Function: BiochemicalProperties of the RecA1, RecA13, and RecA56 Proteins and the Effect ofRecA56 Protein on the Activities of the Wild-type RecA Protein FunctionIn Vitro, Journal of Molecular Biology 234:72 (1993) demonstrated thatthis mutant is inactive in vitro. As discussed below, the substitutionoccurs at a special location in the MAW structure, and the phenylalanineis insufficiently large to affect the activity of the protein in thisposition.

In A. J. Clark, The Beginning of a Genetic Analysis of RecombinationProficiency, Journal of Cellular Physiology 70:165 (1967), a RecA56mutant within the MAW motif is disclosed. This mutant substitutescysteine for arginine at position 60 (60RC). This mutant was shown inthe original disclosure to be inactive in vivo. It has also been shownto be inactive in vitro. See S. D. Lauder and S. C. Kowalczykowski,Negative Co-dominant Inhibition of RecA Protein Function: BiochemicalProperties of the RecA1, RecA13, and RecA56 Proteins and the Effect ofRecA56 Protein on the Activities of the Wild-type RecA Protein FunctionIn Vitro, Journal of Molecular Biology 234:72 (1993). This substitutionis from a volumetrically larger to a smaller residue.

Other mutants in the MAW motif have been disclosed in Ustilago maydisfungi. See B. P. Rubin, D. O. Ferguson, and W. K. Holloman, Structure ofREC2, a Recombinational Repair Gene of Ustilago maydis, and Its FunctionIn Homologous Recombination Between Plasmid and Chromosonal Sequences,Molecular and Cellular Biology 14:6287 (1994). This work disclosed fivemutants within the MAW motif: rec2-4, substituting alanine for serine atposition 42 (42SA); rec2-5, substituting alanine for aspartate atposition 48 (48DA); rec2-2, substituting phenylalanine for leucine atposition 51 (51LF); rec2-6, substituting alanine for glycine at position54 (54GA); and rec2-7, substituting alanine for glycine at position 55(55GA). The 42SA and 55GA mutants involve volumetrically small (alanine)substitutions and behave like the wildtype protein. The 48DA, 51LF, and54GA mutants are defective in UV damage repair as compared to thewildtype protein. 48DA and 54GA involve volumetrically smallsubstitutions. Although 51LF involves a larger (phenylalanine)substitution, it is located at a geometrically special position in thethree-dimensional structure of the MAW motif, and is insufficientlylarge to enhance the DNA binding properties of the protein.

Other E. coli protein mutants are known which bind DNA better than thewildtype protein. See P. E. Lavery and S. C. Kowalczykowski, BiochemicalBasis of the Constitutive Repressor Cleavage Activity of RecA730Protein: A Comparison to RecA441 and RecA803 Proteins, Journal ofBiological Chemistry 267:20648 (1992), and M. V. V. S. Madiraju, P. E.Lavery, S. C. Kowalczykowski, and A. J. Clark, Enzymatic Properties ofthe RecA803 Protein: A Partial Suppressor of recF Mutations,Biochemistry 31:10529 (1992). These publications disclose substitutionof methionine for valine at position 37 (37VM) in RecA803, substitutionof lysine for glutamate at position 32 (32EK) in RecA441, andsubstitution of valine for isoleucine at position 298 (298IV) inRecA441. These publicly available RecA803 and RecA441 mutants bind DNAmore quickly than wildtype RecA. However, these mutants still require anATP-like cofactor.

Similarly, the substitution of aspartate for glutamate at position 96(96ED) in RecA is disclosed in M. J. Campbell and R. W. Davis, On the InVivo Function of the RecA ATPase, Journal of Molecular Biol. 286:437(1999). 96ED allows the mutant RecA protein to bind ATP and prevent itshydrolysis, thus keeping the mutant RecA active. However, this mutant isnot free of the requirement for the ATP cofactor.

It is desirable to produce a cofactor-independent RecA protein. It isalso desirable to produce a RecA protein which binds DNA better thanwildtype RecA. The above listed mutants do not meet these goals becausethey are either inactive, or because they still require a cofactor toactivate.

BRIEF SUMMARY OF THE INVENTION

The invention presents RecA homolog protein mutants wvhich havemutations within the MAW motif. The MAW motif is highly conserved amongvarious species, as shown in the sequence analysis of A. I. Roca & M. M.Cox, Progress in Nucleic Acid Research and Molecular Biology 56:129-223(1997). The MAW motif is defined as amino acid residues 40 to 65 in theEscherichia coli (E. coli) RecA protein (SEQ ID NO: 1) and the homologsof this structure in other proteins. Therefore, as used throughout, theterm “RecA homolog protein” refers to an E. coli RecA protein having theMAW sequence at residues 40-65, inclusive, as shown in SEQ ID NO: 1, ora homolog thereof. These homologs include, but are not limited to,homologs in bacteria, viruses, archaea, and eukaryotes (in particular,human). Examples of these RecA homolog proteins are: bacteria (e.g., E.coli) RecA proteins; viruses (e.g., bacteriophage T4) UvsX proteins;Archaea (e.g., Methanococcus jannaschii) RadA proteins; and Eucarya(e.g., Homo sapiens) Rad51, Dmc1, and Lim15 proteins. In each of theseRecA homolog proteins, the MAW motif is identified as the structuralhomolog of the E. coli RecA MAW motif. (See SEQ ID NO: 1; Roca & Cox,supra).

The mutations of this invention modify the MAW region's properties as anATP-induced conformational switch and as a DNA binding site of the RecAprotein. These mutations involve lo selectively replacing one or morenaturally occurring amino acid residues within the MAW motif withvolumetrically larger residues (Class V mutants), or by replacing one ormore naturally occurring residues with aromatic residues (Class VImutants). Class V mutants are mutants which will be active independentlyof cofactors such as ATP or ATPγS. To achieve this goal, the replacementresidue must be sufficiently large, that is, as large or larger thanphenylalanine.

Thus, the term “RecA homolog protein mutant” as used herein refers to anE. coli RecA protein, or a bacterial, eukaryotic, archaeal, or viralhomolog thereof, in which the naturally occurring MAW motif has beenmodified by one or more such replacements of amino acid residues.“Volumetrically larger,” as used herein in reference to a replacementresidue, means a residue which is larger than the residue it replaces,and which is as large or larger than phenylalanine.

Because the MAW motif is three-dimensional, the selective positioning ofan amino acid residue replacement will affect the physical structure ofthe MAW motif in a RecA homolog protein mutant. Thus, selective positionof such replacements will also affect the behavior of a RecA homologprotein mutant, and this positioning can be controlled to produceparticular results. As referred to herein, “Class V mutants” are thosemutants which will generally reduce the dependence of the RecA homologprotein mutant on the presence of ATP to initiate DNA binding. Examplesof Class V mutants are those with replacements at residues 43, 52, 53,54, 55, or 59, or combinations thereof. Similarly, “Class VI mutants”are those mutants which will generally-bind DNA more tightly than thewildtype RecA homolog proteins from which they are derived. Examples ofClass VI mutants are those with aromatic replacements at residues 40,42, 44, 47, 50, 51, or 56, or combinations thereof. However, thethree-dimensional structure of the MAW motif is such that positions 47and 51 are “special”sites, requiring a sufficiently volumetrically largearomatic substitution, that is, tryptophan, to meet this goal.Combinations of Class V and Class VI mutations are referred to herein as“Class VII mutants,”and will generally exhibit the advantages of Class Vand Class VI mutants.

In creating Class V mutants, replacement amino acid residues areselectively volumetrically larger than the wildtype residues which theyreplace to force structural alterations within the three-dimensional MAWmotif, and sufficiently volumetrically large to place the protein in an“open and active” state. Therefore, those skilled in the art willrecognize that preferable replacement amino acid residues in Class Vmutants will be selected from the group of phenylalanine, lysine,tyrosine, arginine, and tryptophan. In creating Class VI mutants,naturally occurring residues are replaced with aromatic residues.Accordingly, those of skill in the art will recognize that preferablereplacement amino acid residues in Class VI mutants will be selectedfrom the group of tryptophan, tyrosine, phenylalanine, and histidine.Because of the special nature of positions 47 and 51, it will berecognized that, for these positions, tryptophan is the only aromaticreplacement which will be sufficiently large to enhance DNA binding. Forexample, substitution of tyrptophan for leucine at position 47 (47LW) isactive whereas substitution of tyrosine in this position (47LY) is not.This situation is in contrast to that at position 56, where substitutionby either tyrosine (56LY) or tryptophan (56LW) is active. (See FIG. 2).In both Class V and VI mutants, tryptophan is the most preferredreplacement amino acid residue.

It is an object of this invention to provide RecA homolog proteinmutants which are ATP- independent and which can replace RecA inapplications which currently require ATP.

It is a further object of this invention to provide RecA homolog proteinmutants which provide tighter DNA binding compared to wildtype RecA.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a schematic representation of the MAW motif and itsdistribution in the bacterial, viral, archaeal, and eukaryotic RecAhomologs, together with a schematic representation of certain RecAmutants.

FIG. 2 is a graph showing LexA cleavage assay results for examples ofMAW mutants and providing comparisons with wildtype RecA results andresults in the absence of RecA.

FIG. 3 is the SDS-PAGE visualization of purified MAW mutant RecA 491W,giving a comparison of each major fraction (25 μg) from the STL2669strain 49IW preparation.

DETAILED DESCRIPTION OF THE INVENTION

1) Overview

The invention presents RecA homolog protein mutants which have mutationswithin the MAW motif. These mutants may be produced in RecA homologproteins, including those of organisms whose MAW sequences are comparedin FIG. 1. The MAW motif is found in all the listed RecA proteins andtheir homologs.

As an illustration, FIG. 1 schematically presents the sequence of theMAW motif and its distribution in the bacterial, viral, archaeal, andeukaryotic RecA homologs. The data was obtained by applying the sequencealignment method described in A. I. Roca & M. M. Cox, Progress inNucleic Acid Research and Molecular Biology 56:129-223 (1997) and thedata was used to produce FIG. 1. In the line labeled “MAW motif”,uppercase letters represent invariant residues. (See SEQ ID NO: 2).Lowercase letters represent semiconservative changes. (See SEQ ID NO:3). A triangle (Δ) represents a one-residue deletion. “{circumflex over(0)}” indicates an insertion of one or more amino acid residues. Thepositions of the secondary structural elements are indicated by thickhorizontal lines and are labeled “α helix B” and “β strand 1” asdetermined by R. M. Story, I. T. Weber & T. A. Steitz, Nature355:318-325 (1992).

The RecA homolog proteins used for the FIG. 1 analysis are thesixty-four bacterial RecA homologs and the 9 eukaryotes, 1bacteriophage, and 1 archaea described in FIGS. 4 and 9 of A. I. Roca &M. M. Cox, Progress in Nucleic Acid Research and Molecular Biology56:129-223 (1997) and the 2 archaeal homologs (Haloferax volcanii and M.Jannaschii) described in S. J. Sandler, L. H. Satin, H. S. Samra, & A.J. Clark, Nucl. Acids Res. 24:2125-2133 (1996). Examples of the RecAhomolog proteins analyzed in FIG. 1 are those from: humans, mice, E.coli, Saccharomyces cerevisiae, Thermus aquaticus, and Bacillussubtilis. Rad51 and Dmc1 are the RecA homologs found in eukaryotes,including humans and Saccharomyces cerevisiae. RecA/Rad51-like are RecAhomologs found in: Arabidopsis thaliana, E coli, Saccharomycescerevisiae, neurospora crassa, Ustilago maydis, Sulfolobus solfataricus,H. volcanii, and M. jannaschii. RecA/Rad51-like includes Rad51,RecA-like, Sms, Rad57, Rad55, Mei3, Rec2, and RadA. Based on knowninformation, one skilled in the art can thus readily identify the MAWmotif in E. coli RecA and its homologs.

The MAW mutants listed in FIG. 1 are examples of the mutants of theinvention. These mutants exemplify E. coli RecA mutants with one or moremutation sites at positions 47, 49, 53, and 56. The mutants of theinvention may have one or more of the mutations indicated.

RecA homolog protein mutants are herein referred to notationally by theresidue position at which the replacement is made, the amino acidresidue which is replaced, and the replacement residue. For example,replacement of isoleucine (I) by tryptophan (W) at position 49 in E.coli is denoted as 49IW. Standard biochemical notations for the aminoacids are used. For the same mutation in a homologous protein, thehomolog's corresponding RecA MAW amino acid position is used. Furtherclassification is provided by denoting whether a particular mutant is amember of Class V, Class VI, or Class VII, as defined above. Forexample, the mutation 53AW, named “SuperRecA,” is a hyperactive Class Vmutant.

Class V mutants are constitutively active RecA homolog protein mutants.Examples of mutants in this class are changes of the alanine at position53 or changes of the glycines at positions 43, 52, 54, 55, and 59 tovolumetrically larger amino acids. The larger amino acids are preferablyphenylalanine, lysine, tyrosine, arginine, and tryptophan, withtryptophan being the most preferred replacement amino acid.

Conservation of a protein sequence motif (such as the MAW motif) acrossall forms of life correlates with a protein structural role or aligand-binding function. Class V positions are conserved for the proteinstructural role of enabling the ATP induced conformational change. Inwildtype RecA, the MAW motif is buried in the crystal structure whichrepresents the ADP conformation of the RecA protein, that is, closed andless active. ATP or related cofactors induce a conformational change inthe RecA protein to an open and active state. The turns in thepolypeptide backbone of the MAW motif, for example, at the glycinepositions, are involved in this conformational change by acting asflexible hinges. Replacement of glycine or alanine with a volumetricallylarger amino acid at the above positions induces the open and activeconformation independent of the ATP cofactor. Thus, Class V mutants areconstitutively active RecA protein mutants, and thereforeATP-independent. ATP-independence has the dual advantages of reducedcost for processes which currently require ATP or ATPγS and theavoidance of toxicity problems which can arise from use of ATPγS.

Class VI mutants make use of the fact known in the art that thealiphatic-aromatic noncovalent interaction (“interpholation”) is weakerthan the aromatic-aromatic noncovalent interaction (“intercalation”) (E.J. Gabbay et al., Specific Interaction of Peptides with Nucleic Acids,Biochemistry 11:3429-3435 (1972); E. J. Gabbay et al., SpecificInteraction of Peptides with Nucleic Acids: Evidence for a SelectiveBookmark Recognition Hypothesis”, Biochemistry 12:4021-4029 (1973); C.Hélène & J.-C. Maurizot, Interactions of Oligopeptides with NucleicAcids, CRC Crit. Rev. Biochem. 10:213-258 (1981)). As used herein,“interpholation” means aliphatic intercalation.

As mentioned above, conservation of a protein sequence motif (such asthe MAW motif) across all forms of life often correlates with aligand-binding function. In this case the ligand is DNA. The amino acidpositions for the Class VI mutant RecA protein (Class VI positions) ofthe MAW motif are conserved for the role of DNA binding. In the E. coliRecA protein, the Class VI positions include residues, such as leucine,isoleucine, threonine and alanine, which interact weakly with DNA viainterpholation. Thus, examples of Class VI mutants are: 40IY, 40IW,42TY, 42TW, 50AY, 50AW, 51LY, and 51LW. The replacement of theseresidues with aromatic residues, such as tryptophan, would increase thestability of RecA-DNA complexes via intercalation. Aromatic residuereplacements include but are not limited to amino acids tryptophan,tyrosine, phenylalanine, and histidine, with tryptophan being the mostpreferred replacement.

2) Uses of the Invention

E. coli RecA protein plays a central role in homologous recombination,post-replication repair, and the SOS response to DNA damage (S. C. WestAnn. Rev. Biochem. 61: 603-640 (1992); C. M. Radding J. Biol. Chem. 266:5355-5358 (1991); A. I. Roca & M. M. Cox, CRC Crit. Rev. Biochem. Molec.Biol. 25: 415-56 (1990)). RecA protein is also a prototype for DNAstrand exchange proteins, i.e. recombinases. Purified RecA protein bindscooperatively and stoichiometrically to single-stranded DNA (ssDNA).

In strand exchange, the active species is a nucleoprotein filamentcontaining one RecA monomer (38 kDa) per 3 bases of ssDNA. ATPhydrolysis is not required for filament formation or pairing to duplexDNA (dsDNA). However, ATP hydrolysis is required for unidirectional DNAstrand exchange, dissociation of the protein, bypass of structuralbarriers in DNA, and 4-strand exchange reactions. One of the more usefulcommercial properties of RecA is its ability to locate and pair a ssDNAsequence to its homologous dsDNA sequence in the presence of ATPγS orATP. This behavior has been exploited to enrich for specific DNAsequences (B. Taidi-Laskowski, et al., Nucl. Acids Res. 16:8157 (1988);S. M. Honigberg, et al., Proc. Nat. Acad. Sci. U.S.A. 83: 9586 (1986);B. Rigas, et al., Proc. Nat. Acad. Sci. U.S.A. 83:9591 (1986)) and toprotect specific DNA sites from methylation or endonuclease cleavage.(L. J. Ferrin & R. D. Camerini-Otero, Science 254:1494 (1991); M. Koob,et al., Nucleic Acids Res 20:5831 (1992))

For example, RecA protein is commonly used in the followingapplications:

-   (1) Enrichment method for genomic cloning (Taidi-Laskowski (1988),    supra; Honigberg (1986), supra; and Rigas (1986), supra);-   (2) Sequence specific cleavage of large segments of DNA, for    example, RecA-assisted restriction endonuclease (RARE), Achilles'    heel cleavage, Ferrin (1991) and Koob (1992), supra;-   (3) D-loop mutagenesis (D. Shortle, et al., Proc. Nat. Acad. Sci.    U.S.A. 77:5375 (1980));-   (4) Coating of DNA with RecA protein to enhance contrast of electron    micrographs (M. A. Krasnow, et al., Nature 304: 559 (1983));-   (5) Isothermal DNA amplification (U.S. Pat. No. 5,223,414, Process    for Nucleic Acid Hybridization and Amplification, Jun. 29, 1993,    to D. A. Zarling, et al.); and-   (6) Gene therapy (U.S. Pat. No.5,719,023, In Situ Hybridization    Method, Feb. 17, 1998, to D. A. Zarling, et al.).

Other applications of the RecA protein are disclosed in the patentsreferenced above. The RecA mutant protein of the present invention canreplace the wildtype RecA protein or other non-MAW RecA mutants in theabove described five applications and the applications described in thereferenced patents. Because these are RecA mutants, they may be usedunder similar conditions as disclosed in the above applications andpatents. One skilled in the art would be able to, without undueexperimentation, make any modifications necessary to accommodate themutants.

A current limitation of using the wildtype RecA protein (commerciallyavailable from Promega, Pharmacia, and New England Biolabs) or othernon-MAW RecA mutants is the need to use a nucleotide cofactor, such asATPγS. This non-hydrolyzable analog of ATP locks the RecA protein intoan active conformation for DNA binding and/or homology search. ATPγS isexpensive and not a common reagent for molecular biology laboratories.Further, isothermal DNA amplification using the wildtype RecA protein islimited in the selection of DNA polymerases that can be used. Currenttechnology can only use polymerases that are not inhibited by ATPγS.ATPγS may be-toxic for in vivo applications.

The invention defines an ATP conformational switch and a DNA bindingsite of the RecA homolog protein (the MAW motif), and provides for amethod for producing mutants in this region to circumvent the need forATPγS. In vivo results of the SuperRecA mutant (53AW) suggest that thismutation is a constitutive RecA mutant with respect to DNA binding. (SeeA. I. Roca, Initial Characterization of Mutants in a UniversallyConserved RecA Structural Motif, Doctoral Thesis, University ofWisconsin, Madison, Wis. (1997) and FIG. 2).

The mutants in the MAW motif of the invention, in which Class V mutants(such as SuperRecA) are novel ATP-independent RecA homolog proteinmutants, enable the applications which traditionally use RecA protein tobe performed with greater ease and less expensively, for example, by notrequiring ATPγS. Further, in the isothermal DNA amplification, the useof SuperRecA will allow other DNA polymerases and associatedprocessivity factors which may improve DNA amplification results.Therefore, the MAW mutants may replace current technology and expand theRecA market. Because these are mutants of RecA protein, they may be usedunder similar conditions as the wildtype or non-MAW mutant RecA proteinsinzits traditional applications.

Class VI RecA protein mutants, due to their stronger (compared towildtype RecA protein) binding to DNA, are useful in any applicationswhich use wildtype RecA protein (or other RecA mutants with a wildtypeMAW motif sequence) which would be improved by having a stronger DNAbinding RecA protein mutant. Such applications which may be improvedinclude the uses of RecA protein coated single-stranded DNA in genetargeting/therapy technology. Methods for using wildtype RecAprotein-mediated homologous DNA targeting in vivo are found in S. C.Kowalczykowski & D. A. Zarling, in Gene Targeting, M. A. Vega, Ed., CRCPress, Inc., Boca Raton, Fla., pp. 167-210 (1994) and U.S. Pat. No.5,763,240, In Vivo Homologous Sequence Targeting in Eukaryotic Cells,Jun. 9, 1998, to D. A. Zarling & E. P. Sena.

The goal of gene targeting/therapy is to use RecA to catalyze homologouspairing of an exogenous single-stranded DNA to its targeted endogenoushomologous double-stranded DNA in vivo. The conditions used to coattargeting polynucleotides with RecA proteins and ATPγS have beendescribed in U. S. patent application Ser. No. 07/755,462 filed Sep. 4,1991 and U.S. patent application Ser. No. 07/520,321, filed May 7, 1990.

By providing a more stable mutant RecA protein coated DNA strand, theinvention decreases the chance of or prevents the dissociation of theRecA protein from the DNA strand before reaching the targeted DNA withinthe cell nucleus.

RecA protein mutants of the invention were produced in accordance withthe procedures of Example 1.

EXAMPLE 1 Creation of RecA Homolog Protein Mutants

1) Bacterial Strains and Molecular Biology Reagents

Bacterial strains and plasmids are listed in Tables 1 and 2,respectively. Strain STL2669, a gift of Susan Lovett (BrandeisUniversity), is an unpublished recA deletion exoI⁻ strain used forpurifying RecA mutants. This strain is available to the public onwritten request to Dr. Lovett. TABLE 1 Bacterial Strains Strain GenotypeSource AIR4 ompT hsdSB gal dcm lon Δ(srl-recA)306::Tn10 † CJ236 dut-1ung-1 thi-1 relA-1 [F′ pCJ105] Bio-Rad Labs DE1663′Δ(recA-srlR)306::Tn10 Δ(lac-argF)U169 sulA211 †† malB::Tn9 thr leu hispro arg lac gal ara xyl mtl [F′ lacI^(Q) lacPL8 lacZ4505::Tn5 proA⁺B⁺][λ cI ind-1 recAo/p::lacZY] JM109 e14⁻ (McrA⁻) Δ(lac-proAB) thi gyrA96endA1 hsdR17 Promega Corp. relA1 supE44 recA1 [F′ traD36 proA⁺B⁺laqI^(Q) Δ(lacZ)M15] STL2669 thr-1 leuB6 proA62F gpt62F supE44 kdgK51rfbD1 ara-14 lacY1 galK2 S. Lovett xyl-5 mtl-1 tsx-33 rpsL31 xonA2(sbcB⁻) Δ(recA-srlR)306::Tn10† A. I. Roca, Initial Characterization of Mutants in a UniversallyConserved RecA Structural Motif, Doctoral Thesis, University ofWisconsin, Madison, WI (1997)†† J. T. Konola, H. G. Nastri, K. M. Logan & K. L. Knight, Mutations atPro⁶⁷ in the RecA Protein P-Loop Motif Differentially Modify CoproteaseFunction and Separate Coprotease from Recombination Activities, J. Biol.Chem. 270: 8411-9 (1995)

TABLE 2 Bacterial Plasmids Plasmid Description Source pAIR42 subclone ofrecA amino terminal coding region † for in vitro mutagenesis pAIR50′ssubclone of recA amino terminal coding region †, see Table 3, below withMAW mutations pAIR70′s MAW mutant recA constructs for in vivo assays †,see Table 3, below pAIR79 wildtype RecA overexpression construct †pAIR80′s MAW mutant RecA overexpression constructs †, see Table 3, belowpT7POL26 T7 RNA Polymerase delivery plasmid †† pTRecA103 source of recAN-terminal coding region ††† lacking internal NcoI site pTRecA220wildtype recA construct for in vivo assays †††† pZ150 parent vector ofpTRecA220 †††† A. I. Roca, Initial Characterization of Mutants in a UniversallyConserved RecA Structural Motif, Doctoral Thesis, University ofWisconsin, Madison, WI (1997)†† N. Mertens, E. Remaut & W. Friers, Tight Transcriptional ControlMechanism Ensures Stable High-Level Expression from T7 Promoter-basedExpression Plasmids, Bio/Technology 13: 175-9 (1995)††† K. M. Logan & K. L. Knight, Mutagenesis of the P-loop Motif in theATP Binding Site of the RecA Protein from Escherichia coli, J. Mol.Biol. 232: 1048-59 (1993)†††† M. C. Skiba & K. L. Knight, Functionally Important Residues at aSubunit Interface Site in the RecA Protein from Escherichia coli, J.Biol. Chem. 269: 3823-8 (1994)

E. coli cultures were grown at 37° C. in either liquid or solid LBmedium (See J. Sambrook, E. F. Fritsch & T. Maniatis, Molecular Cloning:A Laboratory Manual (Cold Spring Harbor Laboratory, Cold Spring Harbor,N.Y., 2d ed. 1989)) with the following antibiotic (Sigma) concentrationswhen appropriate: ampicillin (100 μg/ml); kanamycin (40 μg/ml);tetracycline (15 μg/ml); chloramphenicol (25 μg/ml). Restrictionendonucleases were from New England Biolabs. Deoxyadenosine5′-[α-[³⁵S]thio]triphosphate and Sequenase were from Amershani/UnitedStates Biochemicals. Deoxyoligonucleotides were obtained from ResearchGenetics (Huntsville, Ala.). Isopropyl-β-D-thiogalactoside (“IPTG”),mitomycin C (“MMC”), and o-nitrophenyl β-D-galactopyranoside (“ONPG”)were from Sigma. Bradford reagent was from Bio-Rad Labs.

2) Construction of MAW Mutants

A subclone of the wildtype recA ORF encoding only the amino-terminalregion of the RecA protein (from the start codon to the unique PstIsite, 237 bp) was used for mutagenesis. Plasmid pTRecA103 was used asthe source of the subclone since the relevant region of the recA genehad already been modified to make the gene more amenable to subsequentcloning manipulations. First, a silent NcoI site had been introduced atthe recA start codon to allow swapping of the amino-terminal region ofthe recA gene between plasmids. Second, a silent mutation was introducedwithin the amino terminal region to destroy an internal NcoI site thatwould have interfered with cloning. (See K. M. Logan & K. L. Knight,Mutagenesis of the P-loop Motif in the ATP Binding Site of the RecAProtein from Escherichia coli, J. Mol. Biol. 232:1048-59 (1993)). Thisregion of the recA gene was PCR amplified (See K. Mullis & F. A.Faloona, Specific Synthesis of DNA in vitro Via a Polymerase-catalyzedChain Reaction, Methods Enzymol. 155:335-50 (1987)) using an upstreamprimer complementary to the start codon of recA and downstreamsequences. This primer also introduced a BamHI site upstream of thestart codon for cloning purposes. The downstream primer wascomplementary to the PstI region of the recA gene. Standard procedures(See J. Sambrook, E. F. Fritsch & T. Maniatis, Molecular Cloning. ALaboratory Manual (Cold Spring Harbor Laboratory, Cold Spring Harbor,N.Y., 2d ed. 1989)) were used to clone the BamHI to PstI PCR productinto pGEM3Zf(−) using the same restriction sites to create plasmidpAIR42. Both strands of the subclone were sequenced to ensure that noerrors were introduced during the PCR reaction. Dideoxy sequencing (SeeF. Sanger, S. Nicklen & A. R. Coulson, DNA Sequencing WithChain-terminating Inhibitors, Proc. Nat. Acad. Sci., U.S.A. 74:5463-7(1977)) of the double-stranded template (Magic Mini-prep DNApurification system, Promega) was performed using modified T7 DNApolymerase (Sequenase) and commercially available primers (Promega) asdescribed (United States Biochemicals).

Plasmid pAIR42 (See A. I. Roca, Initial Characterization of Mutants in aUniversally Conserved RecA Structural Motif, Doctoral Thesis, Universityof Wisconsin, Madison, Wis. (1997)) was used as the template foroligo-directed mutagenesis (See C. S. Craik, Use of Oligonucleotides forSite-Specific Mutagenesis, BioTech. 12-9 (1985)) using the Kunkelselection method (See T. A. Kunkel, J. D. Roberts & R. A. Zakour, Rapidand Efficient Site-specific Mutagenesis without Phenotypic Selection,Methods Enzymol. 154:367-82 (1987)) as supplied in the Muta-GenePhagemid in vitro mutagenesis kit (Bio-Rad). Briefly, uracil-containingssDNA of pAIR42 was made using strain CJ236. Synthetic oligonucleotidescoding for the desired MAW mutation and, if possible, a nearby silentrestriction endonuclease site change were annealed to the template invitro. DNA polymerization and ligation reactions were performed with T4DNA polymerase and T4 DNA ligase, respectively (Bio-Rad). Mutagenesisreactions were electroporated into strain JM109 using a Bio-RadGene-Pulser as described by the manufacturer. Transformants werescreened by diagnostic restriction digests and dsDNA sequencing. Themutations created and their respective plasmid clones are listed inTable 3. Both strands of the amino terminal MAW mutant subclones(pAIR50's) were sequenced as described above. No errors were detected.Care must be taken in the design of the mutagenesis oligonucleotides andthe screening of isolated mutations by sequencing. This region of therecA gene is rich in guanines and cytosines that canintroduce artifactsin these procedures. In particular, the introduction of a tryptophancodon can exacerbate the GC-richness problem since it is encoded by onlyone codon (TGG). TABLE 3 MAW Mutants and Their Respective Plasmid Clonesover- RecA aa wildtype mutant Nterm in vivo expression position aa(code) aa subclone assay clone clone — — — pAIR42 pTRecA220 pAIR79 47leu (L) trp (W) pAIR50 pAIR70 pAIR80 47 leu tyr (Y) pAIR51 pAIR71 pAIR8149 ile (I) trp pAIR55 pAIR75 pAIR85 53 ala (A) trp pAIR56 pAIR76 pAIR8656 leu trp pAIR52 pAIR72 pAIR82 56 leu tyr pAIR53 pAIR73 pAIR83

Full length recA clones containing the MAW mutants were then created(See Table 3). Separate plasmid clones were constructed for the in vivoassays (pAIR70's) and overexpression system (pAIR80's). The in vivoassay plasmid pTRecA220 encoding the full length wildtype recA gene wasused as the backbone for carrying the different MAW mutants. Forexample, the NcoI to PstI fragment carrying the MAW mutation 47LY frompAIR51 was swapped for the NcoI-PstI wildtype coding region of pTRecA220to create pAIR71. The in vivo assay plasmids were electroporated into E.coli strain DE 1663′. In a similar manner, the MAW mutations were movedinto the overexpression plasmid pAIR79 and kept in strain AIR4 orSTL2669. Hence, the plasmid used to overexpress the MAW mutant 47LY ispAIR81.

RecA protein expression from the pTRecA220 vector is regulated by a tacpromoter. It has been determined that in the absence of inducer, RecAprotein levels from this construct are ≈20X higher than the basal levelof expression from a chromosomal copy of the recA gene (See M. C. Skiba& K. L. Knight, Functionally Important Residues at a Subunit InterfaceSite in the RecA Protein from Excherichia coli, J. Biol. Chem.269:3823-8 (1994)).

EXAMPLE 2 In vivo Results with RecA Mutant 53AW

LexA Cleavage Assay

Strain DE 1663′ carries the lacZ gene under the control of theLexA-regulated recA promoter. Therefore, the measurement ofβ-galactosidase activity is related to the extent of RecA-mediated LexAcleavage. The following quantitative cell extract assay was performedessentially as described (See Konola, et al., J. Biol. Chem. 270:8411(1995)) with the following modifications. Single colonies from a freshlystreaked plate were used to inoculate overnight cultures. A 1:100subculture was grown for ≈2 hours. The cultures were divided in halfwith one half brought to a final concentration of 0.5 μg/ml mitomycin C(“MMC”). MMC is a DNA damaging agent which will activate the RecAprotein and subsequent SOS response in vivo. The incubation wascontinued for 3 hours, then the cultures were chilled on ice for 20 min.Cells were pelleted by centrifugation at 4° C. Cells were resuspended inZ buffer (See Miller, in A Short Course in Bacterial Genetics: ALaboratory Manual and Handbook for Escherichia coli and RelatedBacteria, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.,1992, p. 43) and kept on ice. Cells were lysed by sonication for ≈30 secat 30 Watts using a Branson Sonifer model 450, centrifuged, and storedat 40° C. The β-galactosidase activity in the clarified supernatants wasdetermined using ONPG as described ((See Miller, in A Short Course inBacterial Genetics: A Laboratory Manual and Handbook for Escherichiacoli and Related Bacteria, Cold Spring Harbor Laboratory Press, ColdSpring Harbor, N.Y., 1992, p. 43). The same extracts were also used forBradford assays and therefore the units of activity are defined asOD₄₂₀×vol₅₉₅/(time×vol₄₂₀×OD₅₉₅). The OD₄₂₀ and OD₅₉₅ are read from theβ-galactosidase or Bradford reaction mixture, respectively. “Time”refers to the time of the β-galactosidase reaction in minutes. “Vol”refers to the volume of the culture (in milliliters) used in the assayfor either the β-galactosidase or Bradford reaction. This unitdefinition differs from both the classical “Miller” units (See Miller,in A Short Course in Bacterial Genetics: A Laboratory Manual andHandbook for Escherichia coli and Related Bacteria, Cold Spring HarborLaboratory Press. Cold Spring Harbor, N.Y., 1992, p. 43) as well as theprotocol from which these strains were taken (See Konola, et al., J.Biol. Chem. 270:8411 (1995)). Extract from the control strain DE1663′pTRecA220 was prepared fresh along with samples for each experiment. Ithas been determined that a 3 hour incubation time after MMC treatmentyields maximal assay activity with this strain and plasmid combination(See Konola, et al., J. Biol. Chem. 270:8411 (1995)). The experiment wasrepeated three times for each mutant examined.

Results of the experiments are reflected in FIG. 2. FIG. 2 shows resultsusing E. coli strain DE1663′ (recA deletion) transformed with plasmidsexpressing the MAW mutants 47LW, 47LY, 56 LW, 56LY, 49IW, and 53AW,wildtype RecA, and parent vector (pZ150), which were assayed asdescribed above for β-galactosidase activity. Cultures were assayed inthe absence or presence (shaded) of 0.5 μg/ml mitomycin C as indicated.Note that, in the presence of MMC, RecA activity increases for thewildtype and mutant proteins except for 47LY. In the absence of RecA orwith a defective mutant (i.e., 47LY), only background levels of activityare observed after MMC treatment. The hyperactive SuperRecA mutant(53AW) displays activity in the absence of DNA damage. Units are definedas the ratio of absorbance (420/595 nm) readings from theβ-galactosidase and Bradford assays. Values are the average of threeexperiments and the standard error is indicated in the figure.

EXAMPLE 3 Purification of RecA Mutant 49IW

1) Overexpression and Fermentation

A derivative of E. coli strain BL21 (Novagen) was created to remove thechromosomal recA gene. This would prevent the wildtype RecA protein fromcontaminating MAW mutant protein preparations. The construction of thisnew strain, AIR4, is described in A. I. Roca, Initial Characterizationof Mutants in a Universally Conserved RecA Structural Motif, DoctoralThesis, University of Wisconsin, Madison, Wis. (1997), Appendix 2. TheMAW mutant overexpression constructs have the appropriate ORF with nojunction cloning artifacts inserted into the pET21d vector (Novagen,Madison, Wis.). Thus, transcription is controlled by the T7 RNApolymerase (RNAP) from the T7 Ø10 promoter (See Studier, et al., MethodsEnzymol. 185:60 (1990)). The T7 RNAP is delivered by a separate plasmid,pT7POL26, which tightly regulates transcription of T7 RNAP via IPTGinduction (See Mertens, et al., Bio/Technology 13:175 (1995)).

Overexpression of MAW mutants using a fermenter were generally performedin the following manner. A single colony from freshly electroporatedcells (strain AIR4) was used to inoculate a 30 ml culture of LB with ahigh antibiotic selection of 400 μg/ml ampicillin and 40 μg/ml kanamycinfor overnight incubation in a shaken flask. The cells from the saturatedculture were pelleted and resuspended in fresh LB with antibiotics. Theresuspended cells were used to subculture 500 ml of the same medium at astarting OD₆₀₀ of ≈0.1. The culture OD₆₀₀ was closely monitored until avalue of ≈0.5 was reached. This subculture was then used to inoculate 5liters of TB (See Sambrook, et al., Molecular Cloning: A LaboratoryManual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., ed.2nd, 1989)) without antibiotic selection in a New Brunswick Bioflo 3000bench top fermenter. The following parameters on the fermenter wereused: temperature 37° C., pH ≈7.5, air flow 30 liters/min, dissolvedoxygen 20%, and automatic agitation (200-800 rpm) was set to maintainthe desired DO level. When the OD₆₀₀ reached ≈5-15, the culture wasinduced with a form; concentration of 0.2% lactose. Incubation wascontinued for another 5 hours before cells were harvested with aMillipore filtration system using a Masterflex Pump and a PelliconCassette. The final OD₆₀₀ was ≈10-40 with a wet cell mass weighing ≈150grams. The cells were quick frozen in liquid nitrogen and stored at −70°C.

An ExoI nuclease deficient strain, STL2669, was also used to overproducethe MAW mutants. Fermenter conditions were similar to the abovedescription except for the following changes. A New Brunswick Scientific60 liter Mobile Pilot Plant fermenter was inoculated with an exponentialphase 3 liter subculture of bacteria. The culture in the fermenter wasinduced at an OD₆₀₀ of 0.5 with 0.1 mM IPTG and outgrown for 3 hours.Cells were harvested with a Sharples continuous flow centrifuge. Thefinal OD₆₀₀ was ≈1 yielding a wet cell mass of ≈200 grams. Proteinoverexpression was induced at a lower OD₆₀₀ than above to minimizeplasmid loss that is problematic in nuclease deficient strains (SeeBassett & Kushner, J. Bateriol. 157:661 (1984)).

2) Biochemical Reagents

The protein concentration of the purified RecA491W MAW mutant wasdetermined by absorbance at 280 nm using a theoretical extinctioncoefficient of ε₂₈₀=0.71 A₂₈₀ ml/mg and a calculated molecular weight of37,919. The extinction coefficient was calculated using previouslydetermined parameters for tyrosines and tryptophans. (See C. N. Pace, F.Vajdos, L. Fee, G. Grimsley, and T. Gray, How to Measure and Predict theMolar Absorption Coefficient of a Protein, Protein Science 4:2411-23(1995)). DEAE-Sepharose FF resin was from Pharmacia Biotech, Inc.Hydroxyapatite BioGel HTP resin was from Bio-Rad. The prepacked PorosHQ/P column was from PerSeptive Biosystems. ATP, polyethyleneimine, andTris were from Sigma. Ammonium sulfate (“AmS”), potassium chloride, andpotassium phosphate were from Fisher. Dithiothreitol was from ResearchOrganics.

3) Buffers

P buffer contained 20 mM potassium phosphate 50% dianion (pH 6.8 at 25°C.), 1 mM dithiothreitol (“DTT”), 0.1 mM ethylenediaminetetraacetic acid(“EDTA”), 10% (w/v) glycerol. R buffer contained 20 mM Tris-HCl 80%cation (pH 7.5), 1 mM DTT, 0.1 mM EDTA, 10% (w/v) glycerol. Buffers weremade from 20X concentrated stocks.

4) Purification

Purification of RecA 49IW was accomplished essentially as described (SeeM. M. Cox, K. McEntee & I. R. Lehman, A Simple and Rapid Procedure forthe Large Scale Purification of the RecA Protein of Escherichia coli, J.Biol. Chem. 256:4676-8 (1981); Q. Shan, M. M. Cox & R. B. Inman, DNAStrand Exchange Promoted by RecA K72R: Two Reaction Phases withDifferent Mg²⁺ Requirements, J. Biol. Chem. 271:5712-24 (1996)) withmodifications. All steps were carried out at 4° C. A 20% (w/v)suspension of thawed STL2669 fermenter cells (8 g) in sucrose solutionwas lysed with a Gaulin Laboratory Homogenizer model 15M-8TA using 3passes at a pressure of 10,000 pounds per square inch. The lysate wasclarified using a Beckman 60Ti rotor spun at 40,000 rpm for 45 min at 4°C. The supernatant was adjusted to an OD₂₆₀ of ≈160 as previouslydescribed (See S. Tateishi, T. Horii, T. Ogawa & H. Ogawa, C-terminalTruncated Escherichia coli RecA Protein RecA5327 has Enhanced BindingAffinities to Single-stranded and Double-stranded DNAs, J. Mol. Biol.223:115-29 (1992)) to create fraction I (115 ml). Polyethyleneimine (5%w/v, pH 7.5) was added to fraction I to a final concentration of 0.5%.The suspension was stirred for 30 min and then centrifuged for 15 min at9000 rpm in a Beckman JA14 rotor. The pellet was washed with Rbuffer+150 mM AmS. The suspension was stirred and centrifuged as before.The mutant RecA protein was extracted from the pellet with R buffer+300mM AmS after stirring and centrifugation. This RecA-containingsupernatant was set aside. The pellet was re-extracted with the same AmSsolution as before. The supernatants were combined and solid AmS (0.28g/ml) was slowly added. The suspension was left to stir overnight. Thesuspension was centrifuged at 13,000 rpm for 30 min using the JA14rotor. The pellet was washed with R buffer+0.28 g/ml AmS and centrifugedas before. This wash was repeated two more times. The final pellet wasgently resuspended in R buffer+50 mM KCl and dialyzed against 3×1 literof the same buffer to generate fraction II (32 ml, 330 mg of protein).

Fraction II was loaded at a protein concentration of ≈5 mg/ml onto aDEAE-Sepharose FF column (2.5×16 cm) equilibrated in R buffer+50 mM KCl.The column was washed with R buffer+50 mM KCl at a linear velocity of 13cm/h. Mutant RecA protein was monitored by SDS-PAGE. The pooled flowthrough protein peak (fraction III, 49 ml, 125 mg protein) was loadeddirectly onto a hydroxyapatite column (2.5×11.5 cm) pre-equilibrated inP buffer at a protein concentration of 2.5 mg/ml as previously described(See T. Shibata, R. P. Cunningham & C. M Radding, Homologous Paring inGenetic Recombination: Purification and Characterization of Escherichiacoli RecA Protein, J. Biol. Chem. 256:7557-64 (1981)). The column waswashed extensively with P buffer and developed with a 10 column volumephosphate gradient from 20 to 200 mM at a linear velocity of 17 cm/h.Nuclease free fractions were pooled and dialyzed against 3×1 liter of Rbuffer+50 mM KCl to generate fraction IV (130 ml, 64 mg protein).Fraction IV was applied to a 0.8 ml Poros HQ/P FPLC column for severalruns using a superloop. The column was washed with 3 ml R+50 mM KClbuffer and then developed with 15 ml of 0.05 to 2 M KCl linear gradient.Peak fractions were pooled and dialyzed against 2×2 liters of R bufferto yield the final; fraction V (8.4 ml, 45 mg protein). Aliquots of thefraction were frozen in liquid nitrogen and stored at −70° C. indifferent freezers. The RecA 491W mutant protein was at least 99% pureas judged by a densitometric scan of a Coomassie Blue-stained SDS-PAGEgel that was loaded with ≈25 μg of protein. The concentration of themutant was determined using the extinction coefficient described above.This particular protein preparation was free of detectable endo- orexonucleases.

FIG. 3 shows the SDS-PAGE visualization of purified MAW mutant RecA49IW, giving a comparison of each major fraction (25 μg) from theSTL2669 strain 49IW preparation. The four fractions shown in FIG. 3 are:

-   -   I. Clarified lysate.    -   II. The 300 mM AmS extraction from the polyethyleneimine pellet.    -   III. The flowthrough from the DEAE-Sepharose column.    -   IV. The concentrated pool from the phosphate gradient peak off        the hydroxyapatite column.

Those skilled in the art will understand that the descriptions aboveallow the use of other purification methods, such as by modifying themethods found in S. M. Cotterill, et al., Biochemistry 21: 4332 (1982);M. M. Cox, et al., J. Biol. Chem. 256: 4676 (1981); T. Shibata, et al.,J. Biol. Chem. 256: 7557 (1981); J. Griffith & C. G. Shores,Biochemistry 24: 158 (1985); and Q. Shan, et al., J. Biol. Chem. 271:5712 (1996).

Although the invention has been described in detail by way ofillustration and example for purposes of clarity and understanding,modifications, and changes which are within the skill of those skilledin the art are considered to fall within the scope of the invention.

1-27. (canceled)
 28. A purified nucleic acid molecule encoding a mutantRecA protein comprising SEQ ID NO: 3 and having an enhanced DNA bindingactivity compared to an unmutated RecA protein from the same source,wherein a naturally occurring amino acid residue, located within saidsequence, is replaced with an amino acid residue which is volumetricallylarger than the replaced amino acid residue.
 29. The purified nucleicacid molecule of claim 1, wherein said replacement occurs at residue 4of SEQ ID NO:
 3. 30. The purified nucleic acid molecule of claim 1,wherein said replacement occurs at residue 13 of SEQ ID NO:
 3. 31. Thepurified nucleic acid molecule of claim 1, wherein said replacementoccurs at residue 14 of SEQ ID NO:
 3. 32. The purified nucleic acidmolecule of claim 1, wherein said replacement occurs at residue 15 ofSEQ ID NO:
 3. 33. The purified nucleic acid molecule of claim 1, whereinsaid replacement occurs at residue 16 of SEQ ID NO:
 3. 34. The purifiednucleic acid molecule of claim 1, wherein said replacement occurs atresidue 20 of SEQ ID NO:
 3. 35. The purified nucleic acid molecule ofclaim 1, wherein said replacement amino acid residue is selected fromthe group of phenylalanine, lysine, tyrosine, arginine, and tryptophan.36. The purified nucleic acid molecule of claim 2, wherein saidreplacement amino acid residue is selected from the group ofphenylalanine, lysine, tyrosine, arginine, and tryptophan.
 37. Thepurified nucleic acid molecule of claim 3, wherein said replacementamino acid residue is selected from the group of phenylalanine, lysine,tyrosine, arginine, and tryptophan.
 38. The purified nucleic acidmolecule of claim 4, wherein said replacement amino acid residue isselected from the group of phenylalanine, lysine, tyrosine, arginine,and tryptophan.
 39. The purified nucleic acid molecule of claim 5,wherein said replacement amino acid residue is selected from the groupof phenylalanine, lysine, tyrosine, arginine, and tryptophan.
 40. Thepurified nucleic acid molecule of claim 6, wherein said replacementamino acid residue is selected from the group of phenylalanine, lysine,tyrosine, arginine, and tryptophan.
 41. The purified nucleic acidmolecule of claim 7, wherein said replacement amino acid residue isselected from the group of phenylalanine, lysine, tyrosine, arginine,and tryptophan.
 42. A purified nucleic acid molecule encoding a mutantRecA protein comprising SEQ ID NO: 3 and having an enhanced DNA bindingactivity compared to an unmutated RecA protein from the same source,wherein a naturally occurring amino acid residue, located within saidsequence, but excluding residues 8 and 12 of SEQ ID NO: 3, is replacedwith an aromatic amino acid residue.
 43. The purified nucleic acidmolecule of claim 15, wherein said replacement occurs at residue 1 ofSEQ ID NO:
 3. 44. The purified nucleic acid molecule of claim 15,wherein said replacement occurs at residue 3 of SEQ ID NO:
 3. 45. Thepurified nucleic acid molecule of claim 15, wherein said replacementoccurs at residue 5 of SEQ ID NO:
 3. 46. The purified nucleic acidmolecule of claim 15, wherein said replacement occurs at residue 11 ofSEQ ID NO:
 3. 47. The purified nucleic acid molecule of claim 15,wherein said replacement occurs at residue 17 of SEQ ID NO:
 3. 48. Thepurified nucleic acid molecule of claim 15, wherein said replacementamino acid residue is selected from the group of tryptophan, tyrosine,phenylalanine, and histidine.
 49. The purified nucleic acid molecule ofclaim 16, wherein said replacement amino acid residue is selected fromthe group of tryptophan, tyrosine, phenylalanine, and histidine.
 50. Thepurified nucleic acid molecule of claim 17, wherein said replacementamino acid residue is selected from the group of tryptophan, tyrosine,phenylalanine, and histidine.
 51. The purified nucleic acid molecule ofclaim 18, wherein said replacement amino acid residue is selected fromthe group of tryptophan, tyrosine, phenylalanine, and histidine.
 52. Thepurified nucleic acid molecule of claim 19, wherein said replacementamino acid residue is selected from the group of tryptophan, tyrosine,phenylalanine, and histidine.
 53. The purified nucleic acid molecule ofclaim 20, wherein said replacement amino acid residue is selected fromthe group of tryptophan, tyrosine, phenylalanine, and histidine.
 54. Apurified nucleic acid molecule encoding a mutant RecA protein comprisingSEQ ID NO: 3 and having an enhanced DNA binding activity compared to anunmutated RecA protein from the same source, wherein a naturallyoccurring amino acid residue located at residues 8 or 12 of SEQ ID NO:3, is replaced with a tryptophan residue.